We have file system triggers set on approx 75 folders - most of the time they trigger just fine....but a couple times a week *randomly* they'll just stop firing. A quick service restart resolves the issue, but is there something else we can do to more permanently fix this issue?

We are running AM Pro 11.0.2.22 on Win 2012 R2 64-bit. All triggers are configured to use a local folder (E:\dir\subdir\subdir) and none have filters. We have a default user (specified in Options -> Default Properties) that has sufficient access to the local drive and UNC paths used in the tasks. Tasks are set to run as default user in all states (logged on, logged off, locked). The file system triggers are configured with the "No user required" setting.

Dave,
There is a similar issue #23842 in our system that I have fixed for next release. It will greatly increase reliability, however there is no guarantee if there are way too many files added/removed at the same time.
We use Windows built-in technology so the trigger is using Microsoft technology. I have also added in an Event Log entry so this is reported to user as a warning. Hopefully this will satisfy normal to heavy usage better. As ways to remedy this in current release, their best practices suggest using base directories and shorter directory names since the message is sent through a buffer and longer names fill it quicker. The buffer limit is controlled by them, but I moved us from default so messages are not truncated as easily. They also suggest removing sub-directories and having separate triggers for those.